[R-sig-eco] Query related to maxent file in dismo package

[Li Wen]

HI, Raj

1100 points is not huge. Anyway, there are a number of ways to extract values from raster layers.
1. Suppose you sample points are an excel datasheet of X (longitude) and Y (latitude). Saving it as .csv file, then read it into R as spatial data:
	Samples<-SpatialPoints(read.csv("yourfilename.csv"))
	Extracteddataset<- extract(yourrasterstack, Samples)
2. If you have a shape file (from ArcGIS) of the sample points:
	require(rgdal)	
	Samples<-  readOGR(".", layer="yourshapefilename")  ## without ".shp" and the shp file in your working folder

HTH
Li



-----Original Message-----
From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Rajendra Mohan panda
Sent: Wednesday, 20 August 2014 2:19 AM
To: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] Query related to maxent file in dismo package

Thanks a lot Jon

I have more than 1100 sample points. I want to extract values for 19 variables in Bioclim data for maxent model.
I do not understand if the following code automatically loads bioclim variables grd file or not?

logo <- stack(system.file("external/rlogo.grd", package="raster"))

If I have to go for my downloaded grd files then how shall I do? path to defined (system or any drive etc)

I also face problem to define the point matrix for huge datasets as given in example in dismo package. Is there any easy way out?

#presence data
pts <- matrix(c(48.243420, 48.243420, 47.985820, 52.880230, 49.531423, 46.182616, 54.168232, 69.839163, 73.233228, 63.239594, 45.892154, 43.252326, 28.356155) , ncol=2)

I also request you all to know the way I can use ArcGIS extracted grd/ascii file for my sample points to run maxent in R?

I hope it may help me huge datasets I have. Not sure.

Your kind advise is highly appreciated.



With best Regards
Rajendra M Panda
SWR, IIT Kharagpur


On Tue, Aug 19, 2014 at 5:25 PM, Jon Skoien <jon.skoien at jrc.ec.europa.eu>
wrote:

> It depends what you mean by using Climond data for extracting values, 
> I do not know the data set particularly well.
> But I assume you can use Climond data if you download a format which 
> can be opened by raster. If you want a more specific answer, you need 
> to describe more specific what you want to do. It is generally a good 
> advice to follow the mail-recommendations from the r-help list:
>
> PLEASE do read the posting guidehttp://www.R-project.org/ 
> posting-guide.html and provide commented, minimal, self-contained, 
> reproducible code.
>
> Best wishes,
> Jon
>
>
> On 8/19/2014 11:09 AM, Rajendra Mohan panda wrote:
>
>> Thank you Won and Jon
>>
>> I am now able to put my maxent jar file in appropriate folder.
>> However I have little more confusion on extraction of environmental 
>> variables to R.
>> Can we use Climond data for extract values for use in maxent model in R?
>>
>>
>> With best Regards
>> Rajendra M Panda
>> SWR, IIT Kharagpur
>>
>>
>> On Tue, Aug 19, 2014 at 12:33 PM, Jon Skoien 
>> <jon.skoien at jrc.ec.europa.eu
>> >
>> wrote:
>>
>>    Did you download the maxent.jar file from
>>> http://www.cs.princeton.edu/~schapire/maxent/
>>> and put it in the folder with the name returned by:
>>>
>>>> system.file("java", package="dismo")
>>>>
>>> as described in the man-page of maxent?
>>>
>>> If you have already tried this, you have to describe your problem 
>>> better for anyone to be able to help.
>>>
>>> Best wishes,
>>> Jon
>>>
>>>
>>>
>>> On 8/18/2014 6:42 AM, Rajendra Mohan panda wrote:
>>>
>>> Dear All
>>> What is the procedure to fix maxent jar file in "dismo" java file? I 
>>> am doing it after extracting "dismo" zip file.However, the file is 
>>> not executing. I think some silly mistake is there on my part. I 
>>> would highly appreciate if anyone of advise in this regard.
>>>
>>> With best Regards
>>>   Rajendra M Panda
>>>   SWR, Indian Institute of Technology Kharagpur
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-ecology mailing listR-sig-ecology at r-project.orghttps://
>>> stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>>
>>>
>>>
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>>
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>
>

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